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82 lines
2.1 KiB
82 lines
2.1 KiB
7 years ago
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# Copyright 1999-2017 Gentoo Foundation
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8 years ago
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# Distributed under the terms of the GNU General Public License v2
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EAPI=6
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PYTHON_COMPAT=( python2_7 )
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inherit autotools flag-o-matic python-single-r1 toolchain-funcs
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8 years ago
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DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie2"
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HOMEPAGE="https://ccb.jhu.edu/software/tophat/"
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SRC_URI="https://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz"
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LICENSE="Artistic"
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SLOT="0"
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KEYWORDS="~amd64 ~x86"
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IUSE="debug"
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REQUIRED_USE="${PYTHON_REQUIRED_USE}"
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RDEPEND="${PYTHON_DEPS}
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dev-libs/boost:=[threads]
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dev-python/intervaltree[${PYTHON_USEDEP}]
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dev-python/sortedcontainers[${PYTHON_USEDEP}]
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sci-biology/samtools:0.1-legacy
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sci-biology/bowtie:2"
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DEPEND="${RDEPEND}
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virtual/pkgconfig
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sci-biology/seqan:1.4
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>=sys-devel/autoconf-archive-2016.09.16"
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PATCHES=(
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"${FILESDIR}"/${P}-unbundle-seqan-samtools.patch
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"${FILESDIR}"/${P}-fix-c++14.patch
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"${FILESDIR}"/${P}-python2-shebangs.patch
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)
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src_prepare() {
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default
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# remove bundled libs
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rm -rf src/samtools-0.1.18/ src/SeqAn-1.4.2/ || die
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sed -e "s:samtools_0.1.18:${EPREFIX}/usr/bin/samtools-0.1-legacy/samtools:" \
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-i src/tophat.py src/common.cpp || die
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sed -e "s:/usr/include/bam-0.1-legacy/:${EPREFIX}/usr/include/bam-0.1-legacy/:" \
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-e '/^samtools-0\.1\.18\//d' \
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-e '/^SeqAn-1\.4\.2\//d' \
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-e 's:sortedcontainers/sortedset.py \\:sortedcontainers/sortedset.py:' \
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-e 's:\$(top_builddir)\/src\/::' \
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-i src/Makefile.am || die
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sed -e 's:\$(top_builddir)\/src\/::' -i src/Makefile.am || die
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# innocuous non-security flags, prevent log pollution
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append-cflags -Wno-unused-but-set-variable -Wno-unused-variable
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append-cppflags "$($(tc-getPKG_CONFIG) --cflags seqan-1.4)"
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# remove ancient autoconf archive macros, wreaking havoc,
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# depend on sys-devel/autoconf-archive instead, bug #594810
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rm {ax_boost_thread,ax_boost_base}.m4 || die
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eautoreconf
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}
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src_configure() {
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econf $(use_enable debug)
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}
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src_install() {
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default
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# delete bundled python modules
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local i
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for i in intervaltree sortedcontainers; do
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rm -r "${ED%/}"/usr/bin/${i} || die
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done
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}
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pkg_postinst() {
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optfeature "ABI SOLiD colorspace reads" sci-biology/bowtie:1
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}
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